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- PDB-8amy: High-resolution crystal structure of the Mu8.1 conotoxin from Con... -

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Basic information

Entry
Database: PDB / ID: 8amy
TitleHigh-resolution crystal structure of the Mu8.1 conotoxin from Conus Mucronatus
ComponentsMu8.1 conotoxin
KeywordsTOXIN / conotoxin / antagonist / cav2.3 inhibitor / mu8.1
Function / homologyBICARBONATE ION / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE
Function and homology information
Biological speciesConus mucronatus (invertebrata)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.67 Å
AuthorsMueller, E. / Hackney, C.M. / Ellgaard, L. / Morth, J.P.
Funding support Denmark, 1items
OrganizationGrant numberCountry
Novo Nordisk Foundation Denmark
CitationJournal: Acta Crystallogr.,Sect.F / Year: 2023
Title: High-resolution crystal structure of the Mu8.1 conotoxin from Conus mucronatus.
Authors: Muller, E. / Hackney, C.M. / Ellgaard, L. / Morth, J.P.
History
DepositionAug 4, 2022Deposition site: PDBE / Processing site: PDBE
Revision 1.0Aug 23, 2023Provider: repository / Type: Initial release
Revision 1.1Sep 6, 2023Group: Database references / Category: citation / citation_author
Item: _citation.country / _citation.journal_abbrev ..._citation.country / _citation.journal_abbrev / _citation.journal_id_ASTM / _citation.journal_id_CSD / _citation.journal_id_ISSN / _citation.pdbx_database_id_DOI / _citation.pdbx_database_id_PubMed / _citation.title / _citation.year / _citation_author.identifier_ORCID / _citation_author.name
Revision 1.2Sep 13, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation_author.identifier_ORCID
Revision 1.3Oct 16, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Mu8.1 conotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)10,9038
Polymers10,2041
Non-polymers6997
Water1,26170
1
A: Mu8.1 conotoxin
hetero molecules

A: Mu8.1 conotoxin
hetero molecules


Theoretical massNumber of molelcules
Total (without water)21,80516
Polymers20,4072
Non-polymers1,39814
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
point symmetry operation1
Buried area3230 Å2
ΔGint-51 kcal/mol
Surface area8700 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.860, 52.860, 137.430
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number98
Space group name H-MI4122
Space group name HallI4bw2bw
Symmetry operation#1: x,y,z
#2: -y+1/2,x,z+3/4
#3: y+1/2,-x,z+3/4
#4: x+1/2,-y,-z+3/4
#5: -x+1/2,y,-z+3/4
#6: -x,-y,z
#7: y,x,-z
#8: -y,-x,-z
#9: x+1/2,y+1/2,z+1/2
#10: -y+1,x+1/2,z+5/4
#11: y+1,-x+1/2,z+5/4
#12: x+1,-y+1/2,-z+5/4
#13: -x+1,y+1/2,-z+5/4
#14: -x+1/2,-y+1/2,z+1/2
#15: y+1/2,x+1/2,-z+1/2
#16: -y+1/2,-x+1/2,-z+1/2
Components on special symmetry positions
IDModelComponents
11A-506-

ZN

21A-649-

HOH

31A-670-

HOH

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Mu8.1 conotoxin


Mass: 10203.572 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: toxin / Source: (gene. exp.) Conus mucronatus (invertebrata) / Production host: Escherichia coli (E. coli)

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Non-polymers , 7 types, 77 molecules

#2: Chemical ChemComp-MES / 2-(N-MORPHOLINO)-ETHANESULFONIC ACID


Mass: 195.237 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H13NO4S / Comment: pH buffer*YM
#3: Chemical ChemComp-P4G / 1-ETHOXY-2-(2-ETHOXYETHOXY)ETHANE


Mass: 162.227 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O3
#4: Chemical ChemComp-BCT / BICARBONATE ION


Mass: 61.017 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: CHO3
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Zn / Feature type: SUBJECT OF INVESTIGATION
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 70 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.35 Å3/Da / Density % sol: 47.73 %
Crystal growTemperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6.5
Details: 18% PEG 5000 MME. 0.2 M Ammonium sulfate, 0.1 M MES.

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.976254 Å
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Jun 22, 2019
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.976254 Å / Relative weight: 1
ReflectionResolution: 1.67→34.62 Å / Num. obs: 21222 / % possible obs: 98.87 % / Redundancy: 8.2 % / Biso Wilson estimate: 30.23 Å2 / CC1/2: 0.999 / Rmerge(I) obs: 0.06742 / Rpim(I) all: 0.0232 / Rrim(I) all: 0.07147 / Net I/σ(I): 16.59
Reflection shellResolution: 1.67→1.73 Å / Redundancy: 3.4 % / Rmerge(I) obs: 1 / Mean I/σ(I) obs: 1.03 / Num. unique obs: 1401 / CC1/2: 0.464 / Rpim(I) all: 0.6206 / Rrim(I) all: 1 / % possible all: 91.62

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Processing

Software
NameVersionClassification
PHENIX1.20_4459refinement
xia2data reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 7PX2

7px2


Resolution: 1.67→34.62 Å / SU ML: 0.2612 / Cross valid method: FREE R-VALUE / σ(F): 1.34 / Phase error: 26.8445
Stereochemistry target values: GeoStd + Monomer Library + CDL v1.2
RfactorNum. reflection% reflection
Rfree0.2001 1070 5.04 %
Rwork0.1687 20151 -
obs0.1703 21221 98.15 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.1 Å / Solvent model: FLAT BULK SOLVENT MODEL
Displacement parametersBiso mean: 41 Å2
Refinement stepCycle: LAST / Resolution: 1.67→34.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms680 0 39 70 789
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.015759
X-RAY DIFFRACTIONf_angle_d1.66691027
X-RAY DIFFRACTIONf_chiral_restr0.0681112
X-RAY DIFFRACTIONf_plane_restr0.0123124
X-RAY DIFFRACTIONf_dihedral_angle_d14.8957270
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.67-1.750.31941420.31952273X-RAY DIFFRACTION88.85
1.75-1.840.36421170.32762498X-RAY DIFFRACTION97.32
1.84-1.950.3031970.22712597X-RAY DIFFRACTION99.45
1.95-2.10.22271490.1592542X-RAY DIFFRACTION100
2.1-2.320.20021320.18582573X-RAY DIFFRACTION100
2.32-2.650.19891480.16092555X-RAY DIFFRACTION100
2.65-3.340.18721220.16772562X-RAY DIFFRACTION99.96
3.34-34.620.17931630.14172551X-RAY DIFFRACTION99.71
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
11.041784795840.144581480451-0.706993372570.7423201500040.01437887416590.5813010358820.0328322049888-0.02085950478130.0905151663163-0.0684090206460.019780189331-0.107305339984-0.05984538715010.260717222257-7.72337738295E-50.2103969483170.0119820735009-0.0006184484554390.291902885883-0.01087377513560.2677431098625.65349162518.0994822745949.4275253577
20.6596901619670.1395414732880.5454030921590.8246318957890.007385509740270.463546951135-0.01601440207540.04334825106620.158782627506-0.0641001834058-0.02397668857520.0530211815825-0.02065384241380.1311301922910.0001371245776670.2103599549440.01280537050890.02499738878540.246391423201-0.002221659580370.20588206744217.84333792993.8935189965651.227629439
30.944650068875-0.06344111619890.3031797868710.9796148472640.02030217830440.602232040292-0.0277767688334-0.09345090175050.633024655297-0.07267732229480.0279136394961-0.129021706374-0.4375120069740.330079264016-0.0001543844140820.359697583001-0.08257655528830.02198510498340.318836855895-0.008022407959640.42747109229322.358203160219.596988953951.9191362578
Refinement TLS group

Refine-ID: X-RAY DIFFRACTION / Auth asym-ID: A / Label asym-ID: A

IDRefine TLS-IDSelection detailsAuth seq-IDLabel seq-ID
11chain 'A' and (resid 5 through 28 )5 - 281 - 24
22chain 'A' and (resid 29 through 48 )29 - 4825 - 44
33chain 'A' and (resid 49 through 89 )49 - 8945 - 85

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